It would seem that I've picked a pretty bad time to take a few days away from the blog. I come back from the happy land of Amotivation to find that someone nominated me for Best New Blog over at the Koufax Awards.
I'm flattered by the nomination, but I won't be voting for me. I haven't decided who I will vote for yet, but there are quite a few blogs on the list that are much better than this one. Don't just take my word for it. There are something like 125 nominees right now. Browse the list and you'll probably find some really good blogs that you've never heard of before.
23 January 2006
19 January 2006
Evolution in Action - H5N1 Influenza
The H5N1 strain of influenza, also known as "avian influenza" or "bird flu," has been in the news a lot, so I'm assuming that anyone likely to read this knows more or less what it is. If you don't, there's a five-part series over on the old Aetiology site that covers things in depth (1,2,3,4,5). As new cases of this disease are identified, samples of the virus are being shipped to labs and examined in detail. Viruses are notorious for evolving rapidly, and scientists are closely following the evolution of this particular virus.
A news item in this weeks issue of the journal Nature discusses three mutations that have been found in virus samples collected from victims of the H5N1 outbreak in Turkey. At least two of these mutations, according to the article, appear to make the virus better able to attack humans. All three of these mutations involve substitutions of one amino acid for another in a protein.
Two of the mutations involve a protein that allows the virus to bind to the cells of the organism that it is attacking. The researchers don't yet know if one of them has any effect on the way the virus works. The other definitely does. It makes it easier for the virus to bind to human cells, but at a cost: it makes it harder for the virus to bind to bird cells.
The remaining mutation is found in a protein that the virus uses to copy itself. This one is quite familiar to researchers - it is one of the mutations that was found in the Spanish Flu, which appears to have been an avian influenza strain that evolved into a human strain. According to the Nature article, this change makes it easier for the virus to function in primates.
Researchers say that both of these mutations have been observed before, but these cases mark the first time that they have been found together. It's still not certain what effect they will ultimately have on the way that this virus functions, but this is definitely not a comforting discovery, even if the disease does turn out to be less fatal than feared.
The situation with H5N1 illustrates a number of things quite well. First and foremost, it illustrates the power of both molecular ecology and evolutionary approaches in studies of infectious disease. It also demonstrates the value of studying viruses in other, non-human, systems. Viruses can, have, and will evolve the ability to jump from one species of host to another. Studying viruses in other organisms can provide us with a headstart on identifying and attempting to prevent human outbreaks. Such studies could also provide us with a better understanding of the way that populations of viruses function and evolve. Finally, and most importantly, studies like these clearly indicate something that Tara Smith has been saying over at Aetiology for a while now: we badly need to invest in both our public health system as a whole, and in infectious disease research in particular.
A news item in this weeks issue of the journal Nature discusses three mutations that have been found in virus samples collected from victims of the H5N1 outbreak in Turkey. At least two of these mutations, according to the article, appear to make the virus better able to attack humans. All three of these mutations involve substitutions of one amino acid for another in a protein.
Two of the mutations involve a protein that allows the virus to bind to the cells of the organism that it is attacking. The researchers don't yet know if one of them has any effect on the way the virus works. The other definitely does. It makes it easier for the virus to bind to human cells, but at a cost: it makes it harder for the virus to bind to bird cells.
The remaining mutation is found in a protein that the virus uses to copy itself. This one is quite familiar to researchers - it is one of the mutations that was found in the Spanish Flu, which appears to have been an avian influenza strain that evolved into a human strain. According to the Nature article, this change makes it easier for the virus to function in primates.
Researchers say that both of these mutations have been observed before, but these cases mark the first time that they have been found together. It's still not certain what effect they will ultimately have on the way that this virus functions, but this is definitely not a comforting discovery, even if the disease does turn out to be less fatal than feared.
The situation with H5N1 illustrates a number of things quite well. First and foremost, it illustrates the power of both molecular ecology and evolutionary approaches in studies of infectious disease. It also demonstrates the value of studying viruses in other, non-human, systems. Viruses can, have, and will evolve the ability to jump from one species of host to another. Studying viruses in other organisms can provide us with a headstart on identifying and attempting to prevent human outbreaks. Such studies could also provide us with a better understanding of the way that populations of viruses function and evolve. Finally, and most importantly, studies like these clearly indicate something that Tara Smith has been saying over at Aetiology for a while now: we badly need to invest in both our public health system as a whole, and in infectious disease research in particular.
18 January 2006
Got Cheese?
Apparently not content with merely trumpeting their discontent with news articles as they are released, the Discovery Institute's Media Complaints Division has launched a preemptive whine at the New York Times.
Apparently, a reporter from the Times contacted them looking for comment on a recent pro-evolution piece in L'Osservatore Romano. The Discovery Institute, it would appear, is concerned that the Times might think that this somehow represents a stand that is being taken by the Vatican.
The DI's Rob Crowther quotes fromsome spinan email outlining the real facts of the matter that he sent to the Times' reporter:
An op-ed in the official Vatican newspaper by an Italian evolutionary biologist is certainly not at the same level as a clear and unambiguous statement made by the pontiff. However, the material published in the Vatican newspaper is probably a better barometer of the Catholic Church's position on a subject than the views of some third-rate political and media hacks in Seattle.
Apparently, a reporter from the Times contacted them looking for comment on a recent pro-evolution piece in L'Osservatore Romano. The Discovery Institute, it would appear, is concerned that the Times might think that this somehow represents a stand that is being taken by the Vatican.
The DI's Rob Crowther quotes from
Not surprisingly, The New York Times did not the cover the Pope’s approving mention of intelligent design in one of his Wednesday speeches last November, yet it seems to take seriously as Vatican policy an op-ed by a little known writer published in the L'Osservatore Romano. We reported about this at length ourselves at http://www.evolutionnews.org/2005/11/in_evolution_debate_the_media.htmlThe Discovery Institute is fond of citing this bit of so-called support from the Pope, so it might be good to refresh ourselves on exactly what it was that the Pope said about Intelligent Design:
With the sacred Scripture, the Lord awakens the reason that sleeps and tells us: In the beginning, there was the creative word. In the beginning, the creative word -- this word that created everything and created this intelligent project that is the cosmos -- is also love.According to the DI, "intelligent project" should have been translated as "intelligent design." Call me crazy, but reading that as an unambiguous endorsement for the DI's policies seems to me to be a bit of a stretch. The statement is certainly compatible with ID, but it is equally compatible with theistic evolution, or a number of other positions. It does serve as a reminder that the Catholic Church believes that God is personally and continuously involved in His creation. But that is nothing new - the Church never has, and never will, taken any other position.
An op-ed in the official Vatican newspaper by an Italian evolutionary biologist is certainly not at the same level as a clear and unambiguous statement made by the pontiff. However, the material published in the Vatican newspaper is probably a better barometer of the Catholic Church's position on a subject than the views of some third-rate political and media hacks in Seattle.
17 January 2006
American Pride
My parents are currently visiting Honolulu, and last night my wife and I treated them to a luau. The tourist luaus don't really resemble the kinds of celebrations that locals throw, of course, but an "authentic" tourist luau, complete with Tahitian Hula and a Samoan Fire-knife dancer, should be a part of anyone's visit to Hawaii.
This particular luau took place at the Hale Koa hotel in Waikiki. The Hale Koa ("House of the Warrior") is the hotel at the Ft. DeRussey Armed Forces Recreation Center, and caters to the military. This means that pretty much everyone at the luau has some connection to the armed forces.
The people who set up the luau know this, of course, and they close the luau by recognizing and thanking the veterans of the various wars for their service, then by recognizing those who are currently in the service. The final song is a stirring rendition of Lee Greenwood's Proud to be an American, complete with a standing audience and candles.
Usually (we've taken family to this luau a few times now) I more or less blow off the conclusion. I mean, I stand and sing with everyone else, but it isn't exactly what I'd call a thought-provoking moment. Last night was different.
Last night, I started out by thinking about what I could do to show my pride in this country, and what I could do to defend America and American Values. I tried to join the military some years back, but was medically disqualified, so that was out, but I was still feeling a bit guilty. My wife is on active duty, and does her part, but what do I do? What could I do? Then, as I thought about the last verse of the song, it came to me:
I went home, went online, and joined the ACLU.
That's not quite what you were expecting, was it?
I think that our country is really seriously threatened by terrorism. I think that the physical threat to Americans is very much real, and I think that we do need to use our military to protect ourselves. I disaprove of the way we went into Iraq, but I think that our action in Afghanistan was entirely appropriate - the government there was clearly sheltering and assisting groups that had killed large numbers of Americans, and which had every intention of doing so again. Doing our best to deal with that problem made sense.
The physical threat to Americans from terrorists is still out there, and still very much real. We will need to be alert to the possibility of further terrorist strikes for the forseeable future, because there are people who, for various reasons, hate America and want to kill Americans. But that's only part of the threat.
The threat to America goes far beyond the threat of physical attack. The terrorist activities are intended to - and do - create a level of fear in the public. People want to feel safe, and the threat of terrorism makes us feel unsafe. The danger is that we will do things in order to feel safe that threaten exactly those things that make America special - our civil rights.
The ACLU may be unpopular these days. They are the target of right-wing derision, and their willingness to take up unpopular causes doesn't do much to increase their popularity with most Americans. But now, more than ever, the ACLU and other similar organizations are an essential safeguard against attacks on our civil rights.
Dissent is patriotic. Standing up against the government on issues like illegal wiretapping is not only patriotic, it is a courageous stand against the terrorists. It tells them that we will not sacrifice the things that make America great just to protect ourselves against them. I am proud to be an American, and I am willing to do what I can to protect the things that make America special.
Joining the ACLU is the best way I can think of, at least right now, to do that.
This particular luau took place at the Hale Koa hotel in Waikiki. The Hale Koa ("House of the Warrior") is the hotel at the Ft. DeRussey Armed Forces Recreation Center, and caters to the military. This means that pretty much everyone at the luau has some connection to the armed forces.
The people who set up the luau know this, of course, and they close the luau by recognizing and thanking the veterans of the various wars for their service, then by recognizing those who are currently in the service. The final song is a stirring rendition of Lee Greenwood's Proud to be an American, complete with a standing audience and candles.
Usually (we've taken family to this luau a few times now) I more or less blow off the conclusion. I mean, I stand and sing with everyone else, but it isn't exactly what I'd call a thought-provoking moment. Last night was different.
Last night, I started out by thinking about what I could do to show my pride in this country, and what I could do to defend America and American Values. I tried to join the military some years back, but was medically disqualified, so that was out, but I was still feeling a bit guilty. My wife is on active duty, and does her part, but what do I do? What could I do? Then, as I thought about the last verse of the song, it came to me:
And I gladly stand up,In a sudden moment of clarity, I realized that there was something I could do, even if it wasn't much, to do my part to defend the things that this country stands for.
next to you and defend her still today.
‘ Cause there ain’t no doubt I love this land,
God bless the USA.
I went home, went online, and joined the ACLU.
That's not quite what you were expecting, was it?
I think that our country is really seriously threatened by terrorism. I think that the physical threat to Americans is very much real, and I think that we do need to use our military to protect ourselves. I disaprove of the way we went into Iraq, but I think that our action in Afghanistan was entirely appropriate - the government there was clearly sheltering and assisting groups that had killed large numbers of Americans, and which had every intention of doing so again. Doing our best to deal with that problem made sense.
The physical threat to Americans from terrorists is still out there, and still very much real. We will need to be alert to the possibility of further terrorist strikes for the forseeable future, because there are people who, for various reasons, hate America and want to kill Americans. But that's only part of the threat.
The threat to America goes far beyond the threat of physical attack. The terrorist activities are intended to - and do - create a level of fear in the public. People want to feel safe, and the threat of terrorism makes us feel unsafe. The danger is that we will do things in order to feel safe that threaten exactly those things that make America special - our civil rights.
The ACLU may be unpopular these days. They are the target of right-wing derision, and their willingness to take up unpopular causes doesn't do much to increase their popularity with most Americans. But now, more than ever, the ACLU and other similar organizations are an essential safeguard against attacks on our civil rights.
Dissent is patriotic. Standing up against the government on issues like illegal wiretapping is not only patriotic, it is a courageous stand against the terrorists. It tells them that we will not sacrifice the things that make America great just to protect ourselves against them. I am proud to be an American, and I am willing to do what I can to protect the things that make America special.
Joining the ACLU is the best way I can think of, at least right now, to do that.
16 January 2006
Talk about your first impression.
A News @ nature.com article discusses a study just published in Behaviour and Information Technology. It would appear that people can form snap judgements on websites given a view that is as short as 50 milliseconds. I guess finding a good template is more important than I thought.
11 January 2006
Applications of Evolution 3 - tradeoffs in resistance.
Someone just emailed me a copy of an interesting press release. Some time back, a particular mutation known as CCR5delta32 was identified as conferring greatly increased resistance to HIV in individuals who had two copies of that particular gene (in geek terms, those are individuals homozygous for that particular allele). According to the press release, a group of researchers have discovered that this resistance to HIV comes with a price. The individuals who are homozygous for the CCR5delta32 allele do have greatly increased resistance to HIV, but they also have greatly decreased resistance to the West Nile Virus.
This is interesting (to me, anyway) for a number of different reasons.
First, it shows that whether or not a particular mutation is beneficial, neutral, or harmful doesn't just depend on what the mutation does. It also depends on the conditions that the organism lives in. If this mutation is found in someone who lives in an area where West Nile is absent but HIV is common, then this is a beneficial mutation. If the same exact set of genes are found in someone living in an area where West Nile is common and HIV rare or absent, then the mutation is harmful. The environment is almost always important in determining the net effect that a particular mutation is likely to have on the organism.
I should probably stop for a second to make clear what I mean when I use the word "environment." In this case, I'm not just talking about the climate, or pollution, or the effects that humans are having on the natural world. In evolutionary biology (and ecology and other contexts), the "environment" that a particular organism lives in includes everything outside of the organism that has an effect on it. This includes the climate, of course, but it also includes things like predators, competition with other members of the same species, the presence or absence of alternative food sources, and a host of other such things.
In our case, as a species, our environment includes the various disease-causing agents that we are exposed to. As is the case with other environmental factors, like average temperature and rainfall, this factor can vary widely from one geographical location to another. This is true at both large and small scales. On a large scale, for example, leptospirosis is relatively common in Hawaii, but it is pretty much absent in the Northeastern US. On a smaller scale, strains of bacteria that are resistant to multiple antibiotics are more common in hospitals than they are in most homes.
If you want to look into this further, it gets more complex and more interesting, because pathogens are organisms too (that's arguable with viruses, but for these purposes they act like organisms so we'll treat them as such). Anyway, pathogens are organisms, and whether or not a particular mutation in a pathogen is beneficial will depend on the pathogen's environment. For pathogens that impact humans, humans are an environmental factor. Let's say that a strain of HIV mutates in a way that lets it attack people who have the CCR5delta32 resistance. Is that mutation beneficial? Maybe, but maybe not. It's going to depend on whether or not this gain comes with a corresponding cost, and whether the cost is worth the gain. That's going to depend in part on how common people expressing CCR5delta32 resistance are in that area.
Situations like this are things to keep in mind when you hear creationists and ID proponents making arguments like, "almost all mutations are harmful." Life is complex, environments are complex, and the relationships between organisms and environments are extrordinarily complex. The effects of a mutation will depend on an enormous range of factors, and a change in just one external factor can make a harmful mutation beneficial, or a beneficial mutation harmful.
In this case, this mutation was pretty clearly beneficial in North America just a few years back. Anyone who had two copies of the gene with this mutation was resistant to HIV, and until fairly recently West Nile wasn't present here, so the lack of resistance to West Nile wasn't a big problem. Now, it is entirely possible that the mutation is more harmful than helpful. Both HIV and West Nile are relatively uncommon in the US, but HIV transmission can largely be prevented as long as care and common sense are used, while West Nile transmission takes place through an insect vector, and is much harder to prevent. With West Nile now present in almost the entire country, we may well have seen this mutation change from being beneficial to harmful within just a couple of years.
Whether or not a particular mutation is helpful or harmful is very important to evolutionary studies, because it helps determine whether or not that particular mutant form (allele) of the gene is likely to spread, and whether it is likely to spread through the entire population or just certain geographic areas. If the allele is helpful in some locations and harmful in others, it can actually lead to a situation in which you get genetic differences in different areas of the population. That's cool, because it is one of the many scenarios that can lead to one species dividing into two.
This is a pretty cool finding, even if it isn't good news for the HIV research and treatment community. It has definitely taught us some things that are going to be really important to infectious disease specialists - not least, that the CCR5-inhibitors that are currently being tested in clinical trials may have a really big down-side - but also because it can give us some insight into the complex nature of the interactions between our genes and the environment, and how that impacts evolution.
This is interesting (to me, anyway) for a number of different reasons.
First, it shows that whether or not a particular mutation is beneficial, neutral, or harmful doesn't just depend on what the mutation does. It also depends on the conditions that the organism lives in. If this mutation is found in someone who lives in an area where West Nile is absent but HIV is common, then this is a beneficial mutation. If the same exact set of genes are found in someone living in an area where West Nile is common and HIV rare or absent, then the mutation is harmful. The environment is almost always important in determining the net effect that a particular mutation is likely to have on the organism.
I should probably stop for a second to make clear what I mean when I use the word "environment." In this case, I'm not just talking about the climate, or pollution, or the effects that humans are having on the natural world. In evolutionary biology (and ecology and other contexts), the "environment" that a particular organism lives in includes everything outside of the organism that has an effect on it. This includes the climate, of course, but it also includes things like predators, competition with other members of the same species, the presence or absence of alternative food sources, and a host of other such things.
In our case, as a species, our environment includes the various disease-causing agents that we are exposed to. As is the case with other environmental factors, like average temperature and rainfall, this factor can vary widely from one geographical location to another. This is true at both large and small scales. On a large scale, for example, leptospirosis is relatively common in Hawaii, but it is pretty much absent in the Northeastern US. On a smaller scale, strains of bacteria that are resistant to multiple antibiotics are more common in hospitals than they are in most homes.
If you want to look into this further, it gets more complex and more interesting, because pathogens are organisms too (that's arguable with viruses, but for these purposes they act like organisms so we'll treat them as such). Anyway, pathogens are organisms, and whether or not a particular mutation in a pathogen is beneficial will depend on the pathogen's environment. For pathogens that impact humans, humans are an environmental factor. Let's say that a strain of HIV mutates in a way that lets it attack people who have the CCR5delta32 resistance. Is that mutation beneficial? Maybe, but maybe not. It's going to depend on whether or not this gain comes with a corresponding cost, and whether the cost is worth the gain. That's going to depend in part on how common people expressing CCR5delta32 resistance are in that area.
Situations like this are things to keep in mind when you hear creationists and ID proponents making arguments like, "almost all mutations are harmful." Life is complex, environments are complex, and the relationships between organisms and environments are extrordinarily complex. The effects of a mutation will depend on an enormous range of factors, and a change in just one external factor can make a harmful mutation beneficial, or a beneficial mutation harmful.
In this case, this mutation was pretty clearly beneficial in North America just a few years back. Anyone who had two copies of the gene with this mutation was resistant to HIV, and until fairly recently West Nile wasn't present here, so the lack of resistance to West Nile wasn't a big problem. Now, it is entirely possible that the mutation is more harmful than helpful. Both HIV and West Nile are relatively uncommon in the US, but HIV transmission can largely be prevented as long as care and common sense are used, while West Nile transmission takes place through an insect vector, and is much harder to prevent. With West Nile now present in almost the entire country, we may well have seen this mutation change from being beneficial to harmful within just a couple of years.
Whether or not a particular mutation is helpful or harmful is very important to evolutionary studies, because it helps determine whether or not that particular mutant form (allele) of the gene is likely to spread, and whether it is likely to spread through the entire population or just certain geographic areas. If the allele is helpful in some locations and harmful in others, it can actually lead to a situation in which you get genetic differences in different areas of the population. That's cool, because it is one of the many scenarios that can lead to one species dividing into two.
This is a pretty cool finding, even if it isn't good news for the HIV research and treatment community. It has definitely taught us some things that are going to be really important to infectious disease specialists - not least, that the CCR5-inhibitors that are currently being tested in clinical trials may have a really big down-side - but also because it can give us some insight into the complex nature of the interactions between our genes and the environment, and how that impacts evolution.
This is interesting...
...apparently, yesterday's post about Casey Luskin's attempt to have his cake and eat it too may have actually been illegal. The only question is whether or not this blog qualifies as "anonymous." I don't use my name here, but I do over on Panda's Thumb.
10 January 2006
Spinning creationism back into the classroom
It didn't take long for the Discovery Institute to try to call "Darwinists" intolerant for attempting to keep religious advocacy out of the schools. Casey Luskin discusses, over at the Discovery Institute's Media Complaints Division, the lawsuit that Americans United for the Separation of Church and State just filed against a California school. (Ed Brayton discusses this suit in depth over at Dispatches from the Culture Wars.)
According to Casey, because the course is listed as a philosophy class, objecting to it, "represents the true heart of these Darwinists: they don't care about keeping religion out of the science classroom, their goal is to censor any non-evolutionary views in ANY venue regardless of whether or not it is religion or science!!" This misrepresents the actual situation.
The title of the course is "Philosophy of Design," but even Casey admits that there are some problems with that title:party line on definition of Intelligent Design, he goes on to castigate "Darwinists" for trying to exclude ID from schools:
Near the end of his diatribe, Casey poses a question, "What objection could one possibly have to having students learn about material some people consider religious in a philosophy course?" Casey clearly thinks that this question has a clear answer:
First, let's be clear about one thing: this is not a class that is having students "learn about material that some people consider religious." As Casey admits, this is a class that "advocates for young-earth creationism and teaches out of the Bible. [emphasis mine]" Advocating for something is not the same as teaching about it.
Second, the young-earth creationist position is not "material that some people consider religious." It is a religious position. You need look no further than the various statements of faith that the different young-earth groups support to see that.
Casey tries to squirm around the separation of church and state issue with a couple of quotes, neither of which actually applies in this case. In the first, he quotes a passage from a Supreme Court decision: "education is not complete without a study of comparative religion." I actually agree with that, but unless Casey can somehow manage to explain how a class that "advocates for young-earth creationism and teaches out of the Bible," is comparative religion. In the second, he quotes Barry Lynn, the head of Americans United: "when it comes to matters of religion and philosophy, they can be discussed objectively in public schools, but not in biology class." Here, again, Casey needs to show how this course manages to be "objective".
Objecting to having young-earth creationism taught in a public schools isn't a sign of dogmatism about "Darwinism," or about evolution, or about anything to do with science. This is about keeping the state from sponsoring any specific set of religious views at the expense of others. If that's dogmatism, than I guess this is an area where I get dogmatic.
According to Casey, because the course is listed as a philosophy class, objecting to it, "represents the true heart of these Darwinists: they don't care about keeping religion out of the science classroom, their goal is to censor any non-evolutionary views in ANY venue regardless of whether or not it is religion or science!!" This misrepresents the actual situation.
The title of the course is "Philosophy of Design," but even Casey admits that there are some problems with that title:
"The course is misnamed--it actually advocates for young earth creationism and teaches out of the Bible. Such a course would have been more aptly titled something like "Philosophy of Origins" -- but not "Philosophy of design" because intelligent design has nothing to do with young earth creationism or Biblical views."Strangely, though, after admitting that the course doesn't meet the DI's
Rev. Barry Lynn, who leads Americans United for the Separation of Church and State, apparently doesn't want ID even in a philosophy course, because it's too dangerous for young minds to learn about regardless of the venue.Consistency is clearly not a hobgoblin of Casey's mind, regardless of its size. As Casey admits, this is a class that advocates for Young Earth Creationism and which teaches out of the Bible. Casey says that those positions aren't related to Intelligent Design, so why on earth would he think that objecting to a course that does such things is the same as objecting to a class on Intelligent Design?
Near the end of his diatribe, Casey poses a question, "What objection could one possibly have to having students learn about material some people consider religious in a philosophy course?" Casey clearly thinks that this question has a clear answer:
The answer is simple: Darwinists aren't interested in keeping non-evolutionary views just out of the science classroom, they want non-evolutionary views out of students minds completely. If anyone ever doubted the full measure of Darwinist dogmatism, this lawsuit should dispell those doubts.Casey's answer is indeed clearly stated and simple. It is also wrong.
First, let's be clear about one thing: this is not a class that is having students "learn about material that some people consider religious." As Casey admits, this is a class that "advocates for young-earth creationism and teaches out of the Bible. [emphasis mine]" Advocating for something is not the same as teaching about it.
Second, the young-earth creationist position is not "material that some people consider religious." It is a religious position. You need look no further than the various statements of faith that the different young-earth groups support to see that.
Casey tries to squirm around the separation of church and state issue with a couple of quotes, neither of which actually applies in this case. In the first, he quotes a passage from a Supreme Court decision: "education is not complete without a study of comparative religion." I actually agree with that, but unless Casey can somehow manage to explain how a class that "advocates for young-earth creationism and teaches out of the Bible," is comparative religion. In the second, he quotes Barry Lynn, the head of Americans United: "when it comes to matters of religion and philosophy, they can be discussed objectively in public schools, but not in biology class." Here, again, Casey needs to show how this course manages to be "objective".
Objecting to having young-earth creationism taught in a public schools isn't a sign of dogmatism about "Darwinism," or about evolution, or about anything to do with science. This is about keeping the state from sponsoring any specific set of religious views at the expense of others. If that's dogmatism, than I guess this is an area where I get dogmatic.
06 January 2006
Airports and security
I'm sitting at the airport right now - I can really deal with this wireless hotspot thing. Anyway, we got here early enough that getting through security was a breeze. OK, so you have to give your life history to the security folks and submit to a body cavity search, but it really could have been worse.
I was reminded of one thing while we were going through, though, and that's the total and complete exclusion of common sense from the security screening process - particularly when it comes to who to pick for secondary screening. In case you're wondering, I'm not going to advocate for racial profiling, or anything like it. I think it's reasonable to assume that a terrorist could look like pretty much anyone, and I don't think there's any good reason to assume that the next attack (if any) will come from people who look arabic.
But sometimes it would be nice to see some common sense enter the process, if only a little bit. When we (a white family of four) went through security, the person in front of us (also white) was selected for the "secondary screening" patdown. I am aware that a terrorist could look like anyone, but this guy really just didn't seem to fit. I don't know what it was about him that cued me to this. It might have been that he was a very average looking middle-aged white dude. It might have been how tired he looked, or how well mannered. Mostly, though, I think it was the uniform.
Perhaps I'm wrong about this, and maybe nobody should be given a pass. But somehow, it just seems unreasonable to pull a soldier-wearing DCUs and clearly just out of the sandbox-for secondary security screening. Somehow, there's got to be room for common sense in the system somewhere.
I was reminded of one thing while we were going through, though, and that's the total and complete exclusion of common sense from the security screening process - particularly when it comes to who to pick for secondary screening. In case you're wondering, I'm not going to advocate for racial profiling, or anything like it. I think it's reasonable to assume that a terrorist could look like pretty much anyone, and I don't think there's any good reason to assume that the next attack (if any) will come from people who look arabic.
But sometimes it would be nice to see some common sense enter the process, if only a little bit. When we (a white family of four) went through security, the person in front of us (also white) was selected for the "secondary screening" patdown. I am aware that a terrorist could look like anyone, but this guy really just didn't seem to fit. I don't know what it was about him that cued me to this. It might have been that he was a very average looking middle-aged white dude. It might have been how tired he looked, or how well mannered. Mostly, though, I think it was the uniform.
Perhaps I'm wrong about this, and maybe nobody should be given a pass. But somehow, it just seems unreasonable to pull a soldier-wearing DCUs and clearly just out of the sandbox-for secondary security screening. Somehow, there's got to be room for common sense in the system somewhere.
Describing journals
As some of you might know, not all scientific journals are created equal. Some, like Science or Nature, are well known across the entire world, and their articles reach millions. Others, like the Journal of the Pharmacological Society of South-Central Los Angeles, have more narrow foci and restricted audiences. One thing that I've noticed is that scientists sometimes describe different journals almost in code. I've assembled a few observations to help people new to science determine what the description actually means.
If they say.... they really mean....
"It's one of the leading journals in the field."
("They accepted my last manuscript.")
"It's a good journal, but a bit picky sometimes."
("Sooner or later they'll take one of my papers.")
"They're a bit too narrowly focused."
("They rejected my paper without review.")
"Some of the reviewers there can be a little touchy sometimes."
("Four rounds of revisions is too much to take.")
"The lead time is a bit too long."
("Anybody know what happened to the manuscript I submitted in 1999?")
I'll be out of town for a few days, but feel free to add more in the comments.
If they say.... they really mean....
"It's one of the leading journals in the field."
("They accepted my last manuscript.")
"It's a good journal, but a bit picky sometimes."
("Sooner or later they'll take one of my papers.")
"They're a bit too narrowly focused."
("They rejected my paper without review.")
"Some of the reviewers there can be a little touchy sometimes."
("Four rounds of revisions is too much to take.")
"The lead time is a bit too long."
("Anybody know what happened to the manuscript I submitted in 1999?")
I'll be out of town for a few days, but feel free to add more in the comments.
04 January 2006
Somebody needs to buy that man a clue...
...I mean, you'd think that between the family money and the whole President thing, Bush would have one, but this is apparently not the case. I first found this quote via a Maureen Dowd article that my mother sent me, but was quickly able to confirm it on the White House website (both in print and video). One of the things that he said during his opening statement was:
He did. This man, this Commander-in-Chief, actually joked about sustaining an injury in "combat" with a tree while visiting a hospital full of troops that went into, and were injured in, battle at his command. They get shot, stabbed, and bombed. He gets a boo-boo playing at his ranch.
Watching the president's little act was like watching the three-year-old who needs a band-aid because his big brother is getting one, too. It's as if he can't stand the thought of someone else being the focus of attention, or, for that matter, the concept of someone else being more important than him. That man is a disgrace.
As you can possibly see, I have an injury myself -- not here at the hospital, but in combat with a Cedar. I eventually won. The Cedar gave me a little scratch. As a matter of fact, the Colonel asked if I needed first aid when she first saw me. I was able to avoid any major surgical operations here, but thanks for your compassion, Colonel.My first reaction when I read this was that it was a poor, mean-spirited attempt at satire by Dowd. Then I remembered that this is the same man who once literally invited our enemies to attack American troops ("bring 'em on"), and decided to see if he really said it.
He did. This man, this Commander-in-Chief, actually joked about sustaining an injury in "combat" with a tree while visiting a hospital full of troops that went into, and were injured in, battle at his command. They get shot, stabbed, and bombed. He gets a boo-boo playing at his ranch.
Watching the president's little act was like watching the three-year-old who needs a band-aid because his big brother is getting one, too. It's as if he can't stand the thought of someone else being the focus of attention, or, for that matter, the concept of someone else being more important than him. That man is a disgrace.
02 January 2006
Why it matters:
In today's Baltimore Sun, there is an op-ed by New Hampshire Union Leader editorial page editor Andrew Cline. Cline makes an argument that I've heard a lot from religious conservatives lately, that the courts go to far when they rule that government "endorsement" of religion is unconstitutional:
Cline writes:
That's not what the Dover School Board did in their statement. The Dover Board crafted a statement that did not simply mention Intelligent Design; it was clearly written in such a way as to favor Intelligent Design at the expense of evolution. Judge Jones discusses this in one of the sections of his decision:
The policy that Judge Jones declared unconstitutional is a true endorsement of a specific religious viewpoint at the expense of all others, not "the mere practice of pointing it out to students." Cline is definitely tilting at a strawman, not the judge's actual decision. Still, I think it's worth pointing out exactly why the endorsement test is so important, and why this case is such a good example of that importance.
Cline attributes the "endorsement" test to a concurring opinion written by Sandara Day O'Connor in the 1984 case Lynch v. Connoly. Cline managed to avoid mentioning why O'Connor thought that it is inappropriate for government to endorse religion. Personally, I think she provided a very clear and compelling explanation:
To begin with, it is important to remember that while it is possible that evolution is inconsistent with some people's religion, it is not inconsistent with everyone's religion. Some people may be completely happy with evolution being the mechanism used by God to create life, and pushing the "God the inept tinkerer" view of Intelligent Design may be incompatible with their religion. Mr. Stough testified that this was certainly true in his case:
Outside of the issues involving the right of the parents to determine the child's religious upbringing, there are other issues as well, involving what Justice Black referred to as, "the hatred, disrespect and even contempt of those who held contrary beliefs." Early in the trial, Bryan Rehm testified about what he found he had to deal with as a result of standing up for his constitutional rights:
Unfortunately, Bryan Rehm was hardly the only person involved in the dispute to have their religious views attacked. Casey Brown was called an atheist by a member of the school board after resigning in protest over the decision. Another member of the board told her that she would be going to hell. The teachers had to deal with having people believe that they must be atheists if they did not agree with the board. Never mind that "atheist" should not be an insult in America; never mind that it is entirely inappropriate to question people on their religious views when the topic is public education; we have an establishment clause because people who have no religious beliefs should be able to fully participate in their government's actions.
Perhaps better than anyone else, Frederick Callahan summed up what is at stake in cases like this:
I disagree with the wording of that statement. But it defies logic to say it establishes a state religion. And in fact, Judge Jones does not conclude that. Under Establishment Clause jurisprudence, he doesn't have to.I think Cline manages to misunderstand a couple of different things here. He obviously doesn't have a clue about why O'Connor defined the "endorsement" test, or how the circumstances of this case illustrate the value of that standard. He also doesn't seem to grasp exactly what the Dover School Board was attempting to do.
In the 1984 case Lynch v. Donnelly, Supreme Court Justice Sandra Day O'Connor created a new standard that redefined the Establishment Clause. Government policies don't have to "establish" a state religion - as the Constitution requires - to be unconstitutional. They simply have to "endorse" a religious point of view. Justice O'Connor succeeded in rewriting the First Amendment, and Judge Jones used that rewrite to strike down the intelligent design statement.
As the Establishment Clause morphs into a general anti-religion clause and judges continue to strike down not the establishment of religion, or even the teaching of it, but the mere practice of pointing it out to students, it is easy to imagine a day when no reference to God, religion or spirituality will be allowed in school.
Cline writes:
After all, the Dover school board did not replace evolution with intelligent design. The board made students aware of its existence and instructed them to make up their own minds. If that is unconstitutional, then surely it is conceivable that some ambitious parent could sue successfully under the Establishment Clause because a civics teacher quotes George Washington - "The fate of unborn Millions will now depend, under God, on the courage and conduct of this army" - or Abraham Lincoln - "With malice toward none, with charity for all, with firmness in the right as God gives us to see the right, let us strive on to finish the work we are in."This makes it appear that the Board was merely mentioning religion in the statement, and that the policy was struck down on those grounds alone. If that were the case, I might actually agree that the decision was problematic. There are a lot of people out there that have religious concerns regarding evolution, and I think that it is reasonable to mention that at the start of a biology course. I think that it's important to make the difference between science and religion clear to the students, and explain which one you are talking about and which one you should speak to your parents and/or pastor about.
That's not what the Dover School Board did in their statement. The Dover Board crafted a statement that did not simply mention Intelligent Design; it was clearly written in such a way as to favor Intelligent Design at the expense of evolution. Judge Jones discusses this in one of the sections of his decision:
In summary, the second paragraph of the disclaimer undermines students' education in evolutionary theory and sets the groundwork for presenting students with the District's favored religious alternative.It's one thing to mention that people have religious objections to evolution, and that there are religious alternatives available. It's another to denigrate the scientific theory and push a religious one in its place. (It's yet a third to put together a movement dedicated to falsely claiming to do science just to dilute the teaching of evolution, but that's another topic.)
Paragraph three of the disclaimer proceeds to present this alternative and reads as follows:Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.P-124. Students are therefore provided information that contrasts ID with "Darwin's view" and are directed to consult Pandas as though it were a scientific text that provided a scientific account of, and empirical scientific evidence for, ID. The theory or "view" of evolution, which has been discredited by the District in the student's eyes, is contrasted with an alternative "explanation," as opposed to a "theory," that can be offered without qualification or cautionary note. The alternative "explanation" thus receives markedly different treatment from evolutionary "theory."
The policy that Judge Jones declared unconstitutional is a true endorsement of a specific religious viewpoint at the expense of all others, not "the mere practice of pointing it out to students." Cline is definitely tilting at a strawman, not the judge's actual decision. Still, I think it's worth pointing out exactly why the endorsement test is so important, and why this case is such a good example of that importance.
Cline attributes the "endorsement" test to a concurring opinion written by Sandara Day O'Connor in the 1984 case Lynch v. Connoly. Cline managed to avoid mentioning why O'Connor thought that it is inappropriate for government to endorse religion. Personally, I think she provided a very clear and compelling explanation:
Endorsement sends a message to nonadherents that they are outsiders, not full members of the political community, and an accompanying message to adherents that they are insiders, favored members of the political community.O'Connor's explanation is quite similar to one that was provided by Justice Black in an earlier case (I suspect that O'Connor's endorsement criteria were not created ex nihlo, as Cline would have us believe, but were instead a natural evolution of existing precedent.):
The history of governmentally established religion, both in England and in this country, showed that whenever government had allied itself with one particular form of religion, the inevitable result had been that it had incurred the hatred, disrespect and even contempt of those who held contrary beliefs.The testimony of the plaintiffs in the Dover case, unfortunately, illustrates just how right Black was.
To begin with, it is important to remember that while it is possible that evolution is inconsistent with some people's religion, it is not inconsistent with everyone's religion. Some people may be completely happy with evolution being the mechanism used by God to create life, and pushing the "God the inept tinkerer" view of Intelligent Design may be incompatible with their religion. Mr. Stough testified that this was certainly true in his case:
Q. Tell us how you believe you've been harmed.This same concern was voiced by other plaintiffs, including Barrie Callahan and Christie Rehm. Personally, I think it is entirely reasonable for parents to want the government, at all levels, to stay the hell away from the religious education of their children. When the government gets involved in endorsing religious beliefs, you run the risk of having things like this happen:
A. I believe that the actions of the school board in adopting this policy including intelligent design have usurped my authority to be the one in charge of my daughter's religious education.
Intelligent design posits an intelligent designer, which for me they're talking about God. It is a more literal translation of the Bible than I would accept and I plan on teaching my daughter, that type of non-literal interpretation.
Q. And can you tell us what harm you believe that it has caused you?Upsetting is probably putting it mildly.
A. Late in '04 my daughter came home from school, and I was discussing kind of what was going on in the district with her. And she looked at me and she said, Well, Mom, evolution is a lie, what kind of Christian are you, anyway, which I found to be very upsetting.
Outside of the issues involving the right of the parents to determine the child's religious upbringing, there are other issues as well, involving what Justice Black referred to as, "the hatred, disrespect and even contempt of those who held contrary beliefs." Early in the trial, Bryan Rehm testified about what he found he had to deal with as a result of standing up for his constitutional rights:
Now people stare. They know you're a Plaintiff or they know in this particular case that I'm a candidate opposing the school board, and you can't sit there and not worry about who's looking at you or what's going to happen, you know. You'll go out and regularly be called inappropriate things centering around the concept of atheist.That is why we have an establishment clause in the first place. We have an establishment clause to keep people from having to be singled out because of their religious beliefs.
They don't know me. They don't know that I'm the co-director of the children's choir at church or that I run the music halfway at the second service, or that, you know, my wife and I run Vacation Bible School. Yet they have no problem going around calling me an atheist because my particular religious viewpoint doesn't agree with that of the school board, which is a public entity not a religious one.
Unfortunately, Bryan Rehm was hardly the only person involved in the dispute to have their religious views attacked. Casey Brown was called an atheist by a member of the school board after resigning in protest over the decision. Another member of the board told her that she would be going to hell. The teachers had to deal with having people believe that they must be atheists if they did not agree with the board. Never mind that "atheist" should not be an insult in America; never mind that it is entirely inappropriate to question people on their religious views when the topic is public education; we have an establishment clause because people who have no religious beliefs should be able to fully participate in their government's actions.
Perhaps better than anyone else, Frederick Callahan summed up what is at stake in cases like this:
You know, I've read the polls. I think, you know, a lot of people feel that this should be, that this should be in, that it doesn't cross the line. There are a lot of people that don't care. But I do care. It crosses my line.By endorsing a religious view, the Dover School Board overstepped their permitted bounds, and in so doing harmed their community. I don't know how much more clearly I can say that: endorsing a religious view at the expense of others divides people along religious lines. Our founding fathers made sure that we had an establishment clause because they were tired of just that sort of foolishness. Unfortunately, more than 200 years later small minded idiots continue to try to force their views on others. Fortunately, we have (at least for the moment) an independent federal judiciary that can help us protect our rights.
And, you know, I've been -- there have been letters written about the Plaintiffs. We've been called atheists, which we're not. I don't think that matters to the Court, but we're not. We're said to be intolerant of other views.
Well, what am I supposed to tolerate? A small encroachment on my First Amendment rights? Well, I'm not going to. I think this is clear what these people have done. And it outrages me.
30 December 2005
Desparate, pathetic, and disgusting - DI's West on Judge Jones
John West of the Discovery Institute has been critiquing Judge Jones' decision in the Dover ID lawsuit over at the DI Media Complaints Division blog. I haven't, for the most part, addressed these posts, since other Pandas' Thumb regulars have more relevant expertise and have been doing a better job at it than I could. His latest post, however, is so far from the bounds of decency and civility that I can't leave it be. One part in particular, mentioned in passing by PvM in another PT post, hits a new low. In a relatively short passage, West manages to combine a gratuitous personal attack with a view of both what it should mean to be a conservative and on what a lawyer should be proud of that is twisted beyond all recognition.
Here's the passage:
In a sick and twisted sort of way, I almost admire West. He must have put a hell of a lot of time into learning how to be a slippery, lying, son-of-a--. Unless the man was born without a shred of human decency, he would have had to learn how to override those instincts, and that's (fortunately) not something that just anyone is capable of.
For those who haven't figured out exactly where the lie is in that excerpt, I'll highlight it in boldface and mark it with ** at the start and end of the suspect area:
What West did was to selectively omit material, resulting in a passage that looks like it means something a bit different from what the author actually said. Remember, West's take on the quote is that it demonstrates that, "Judge Jones does not seem in sync with most conservatives' attitudes toward crime and punishment." The quote is placed in support of that statement, and is clearly intended to imply that Jones was proud of what he did because of his views on crime and punishment. If the quote is examined in context, however, it paints a slightly different question. Let's start by looking at the question that Jones was answering:
And it was his duty, and he should be proud of that. This country was not founded with the sort of "fry 'em all and let God sort it out mentality" that seems to be promoted by some these days. The founders of this country deliberately decided to use a justice system based on an assumption of innocence, and to make sure that anyone accused of a crime was entitled to a proper defense. Supporting that powerful principle should not be a mark of "liberalism," or indicate that someone doesn't have the "right" view of crime and punishment. Supporting the right of anyone accused of a crime to an adequate defense should be - is - an American Value.
A lawyer who is providing the defense for an accused criminal has the same obligation to the client whether he or she was hired by the accused or assigned the case as a public defender. That obligation is simple and clear: the lawyer must defend the client to the best of their abilities. Nothing less should be acceptable.
John West has become so desparate for ammunition to use to attack the decision and the judge that he is apparently willing to resort to dishonesty and false witness. In this case, he has overstepped the bounds of human decency. He has tried to take a lawyer's account of doing the right thing for a client - a lawyer demonstrating the ideals of the American justice system - and twist it into a "soft on crime" attack.
If West has any remaining hint of human decency, he will apologize and retract that portion of his attack. If he has something that serves as an occasional substitute for human decency, he will at least clarify his post to show why Jones was proud of what he did. I'm not holding my breath waiting for either.
Here's the passage:
In addition, Judge Jones does not seem in sync with most conservatives' attitudes toward crime and punishment. During his confirmation hearings, he spoke with pride about defending a murderer of a twelve-year old boy and how he was able to get the murderer spared from the death penalty:I served for 10 years, Madam Chairwoman, as an assistant public defender in Schuylkill County, and so very frequently I found myself enmeshed in unpopular areas representing unpopular people. In particular, in 1989, I represented an individual who was alleged to have murdered a 12-year-old boy. It was, as you can imagine, coming from a small town, a highly charged atmosphere. We had a week-long trial. I represented him throughout in a most difficult circumstance, with the community at large very much against him. He was convicted. I was able to keep him from suffering the death penalty in that case... I was very proud to do that as an assistant public defender consistent with my obligations as an attorney.
In a sick and twisted sort of way, I almost admire West. He must have put a hell of a lot of time into learning how to be a slippery, lying, son-of-a--. Unless the man was born without a shred of human decency, he would have had to learn how to override those instincts, and that's (fortunately) not something that just anyone is capable of.
For those who haven't figured out exactly where the lie is in that excerpt, I'll highlight it in boldface and mark it with ** at the start and end of the suspect area:
He was convicted. I was able to keep him from suffering the death penalty in that case**...** I was very proud to do that as an assistant public defender consistent with my obligations as an attorney.What a surprise, the lie is in the ellipsis.
What West did was to selectively omit material, resulting in a passage that looks like it means something a bit different from what the author actually said. Remember, West's take on the quote is that it demonstrates that, "Judge Jones does not seem in sync with most conservatives' attitudes toward crime and punishment." The quote is placed in support of that statement, and is clearly intended to imply that Jones was proud of what he did because of his views on crime and punishment. If the quote is examined in context, however, it paints a slightly different question. Let's start by looking at the question that Jones was answering:
Senator Cantwell. Without objection.If nothing else, this indicates that Jones was not responding to a question about his views on punishment in general or on the death penalty in particular. Now, let's look at his whole response, not just the part that paints the picture that West wants people to see. I'll use boldface to indicate the material quoted by West, and I will use italics to indicate the material that is contained within West's ellipsis.
I have one last question for actually all of you, a panel question. Some of our most beloved judges in history have been judges who made decisions that were against popular sentiment, or stood up to protect the rights of minorities or people's whose views made them outcasts.
Can you tell me of an instance in your career where you have stood up, took an unpopular stand, or fought for something, maybe a client, and how you stood up to those pressures?
I served for 10 years, Madam Chairwoman, as an assistant public defender in Schuylkill County, and so very frequently I found myself enmeshed in unpopular areas representing unpopular people. In particular, in 1989, I represented an individual who was alleged to have murdered a 12-year-old boy.Wow. Is it just me, or does the material that West cut from the passage change the meaning just a mite? Jones' isn't saying that he's proud that he kept the guy off of death row, he's saying that he was proud to take on an unpopular case because that was his duty as a public defender.
It was, as you can imagine, coming from a small town, a highly charged atmosphere. We had a week-long trial. I represented him throughout in a most difficult circumstance, with the community at large very much against him. He was convicted. I was able to keep him from suffering the death penalty in that case.
But I learned perhaps more than anything else that I ever did as an attorney about the obligation that we have as attorneys to take on occasionally unpopular cases, and that at that time was the most unpopular case that I could possibly have chosen to have undertaken. And so that stands out amongst all the cases that I ever handled, or matters that I have handled as the most unpopular, but I was very proud to do that as an assistant public defender consistent with my obligations as an attorney.
And it was his duty, and he should be proud of that. This country was not founded with the sort of "fry 'em all and let God sort it out mentality" that seems to be promoted by some these days. The founders of this country deliberately decided to use a justice system based on an assumption of innocence, and to make sure that anyone accused of a crime was entitled to a proper defense. Supporting that powerful principle should not be a mark of "liberalism," or indicate that someone doesn't have the "right" view of crime and punishment. Supporting the right of anyone accused of a crime to an adequate defense should be - is - an American Value.
A lawyer who is providing the defense for an accused criminal has the same obligation to the client whether he or she was hired by the accused or assigned the case as a public defender. That obligation is simple and clear: the lawyer must defend the client to the best of their abilities. Nothing less should be acceptable.
John West has become so desparate for ammunition to use to attack the decision and the judge that he is apparently willing to resort to dishonesty and false witness. In this case, he has overstepped the bounds of human decency. He has tried to take a lawyer's account of doing the right thing for a client - a lawyer demonstrating the ideals of the American justice system - and twist it into a "soft on crime" attack.
If West has any remaining hint of human decency, he will apologize and retract that portion of his attack. If he has something that serves as an occasional substitute for human decency, he will at least clarify his post to show why Jones was proud of what he did. I'm not holding my breath waiting for either.
Evolution in Action
As I mentioned before, Science named evolution as the breakthrough of the year for 2005. There is a good video presentation on the discoveries available on the journal's website. It's definitely worth a look.
29 December 2005
Another round with Krauze
Krauze has replied to my last post in our continuing discussion of some of the finer points of the definition of science used by Judge Jones in the Dover decision. If you haven't been following the discussion so far, it shouldn't be too hard to figure out what's going on. If you want to go back and look at the earlier posts, I linked to all of them in my previous reply.
The series of posts has gotten to be a bit on the long side, and I don't think we've covered too much ground, mostly (I think) because we're talking past each other just a bit. I'll try again to clear up where I think the biggest areas of confusion lie.
Let's start with the passage from the decision that's at the center of our little debate:
I think it's reasonable to say that the core of the original dispute stems from the difference between Krauze's opinion that it is unreasonable to exclude the supernatural from science versus my own belief that the judge acted entirely reasonably. The most recent posts in this debate center, at least for me, around the reasons for the exclusion of the supernatural from science.
Before I get into that in more detail, I'm going to address a criticism Krauze raises in his latest reply. Krauze points out that the designer is not necessarily supernatural, but could be some sort of extraterrestrial being. That's certainly a point worth raising. After all, if ID doesn't actually require a supernatural designer, then the whole question might be moot. The judge considered, and discarded, that possibility. I think he made the right call:
Moving on, Krauze seems to misunderstand one of the main points that I was trying to make last post:
When I raised those points about testability and the supernatural, I was not trying to substitute my own reasoning for that of the judge. I was attempting to explain why there is a "centuries-old ground rule" against invoking the supernatural in science. To put it as plainly and simply as possible, nobody has been able to conduct an empirical test for the hypothesis that "God did it," nobody has been able to design an empirical test for the hypothesis that "God did it," and nobody has been able to conceive of an empirical test for the hypothesis that "God did it."
This line of reasoning was available to the judge when he wrote his opinion. Two different experts testified on this during the plaintiff's case. You can find it in Ken Miller's testimony and in Robert Pennock's testimony.
Noting as an "additionally important" fact the lack of positive tests of ID is also relevant. This does not simply restate the untestable nature of supernatural causes; it also provides a strong indication that ID proponents have not been successful in their attempts at overcoming this limitation. To put it another way, in the absence of a method of positively testing for a supernatural cause, there is absolutely no reason whatsoever to reassess the "centuries-old ground rules of science."
In an attempt to move the discussion into more pragmatic grounds, Krauze presents me with a hypothetical:
I tried to put a little effort into answering this, but, to put it bluntly, I don't find it to be either interesting or realistic. Yes, I think that such a demand from the NSF would be unreasonable, and I think that a scientist in such a situation should strenuously object. I also think that I'll carry an open umbrella with me at all times outdoors if pigs learn how to fly. In both cases, there's something really, really big between the hypothetical that has been posed and current reality.
If you want me to seriously question whether excluding the supernatural is a good ground rule, you are going to need to give me a real reason to reconsider the situation. Come up with a remotely reasonable test, and I'll get interested quick. Until you have that, all of these complaints about how unfair it is to exclude these things are nothing more than sour grapes.
The series of posts has gotten to be a bit on the long side, and I don't think we've covered too much ground, mostly (I think) because we're talking past each other just a bit. I'll try again to clear up where I think the biggest areas of confusion lie.
Let's start with the passage from the decision that's at the center of our little debate:
We find that ID fails on three different levels, any one of which is sufficient to preclude a determination that ID is science. They are: (1) ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; (2) the argument of irreducible complexity, central to ID, employs the same flawed and illogical contrived dualism that doomed creation science in the 1980’s; and (3) ID’s negative attacks on evolution have been refuted by the scientific community. As we will discuss in more detail below, it is additionally important to note that ID has failed to gain acceptance in the scientific community, it has not generated peer-reviewed publications, nor has it been the subject of testing and research. (Decision, p.64)
I think it's reasonable to say that the core of the original dispute stems from the difference between Krauze's opinion that it is unreasonable to exclude the supernatural from science versus my own belief that the judge acted entirely reasonably. The most recent posts in this debate center, at least for me, around the reasons for the exclusion of the supernatural from science.
Before I get into that in more detail, I'm going to address a criticism Krauze raises in his latest reply. Krauze points out that the designer is not necessarily supernatural, but could be some sort of extraterrestrial being. That's certainly a point worth raising. After all, if ID doesn't actually require a supernatural designer, then the whole question might be moot. The judge considered, and discarded, that possibility. I think he made the right call:
Although proponents of the IDM occasionally suggest that the designer could be a space alien or a time-traveling cell biologist, no serious alternative to God as the designer has been proposed by members of the IDM, including Defendants’ expert witnesses. (20:102-03 (Behe)). In fact, an explicit concession that the intelligent designer works outside the laws of nature and science and a direct reference to religion is Pandas’ rhetorical statement, “what kind of intelligent agent was it [the designer]” and answer: “On its own science cannot answer this question. It must leave it to religion and philosophy.” (P-11 at 7; 9:13-14 (Haught)). (Decision, pp.25-6)It's also hard to avoid the conclusion that ID requires a supernatural explanation, particularly for the judge, when all three of the defense expert witnesses said that it does:
Defendants’ expert witness ID proponents confirmed that the existence of a supernatural designer is a hallmark of ID. First, Professor Behe has written that by ID he means “not designed by the laws of nature,” and that it is “implausible that the designer is a natural entity.” (P-647 at 193; P-718 at 696, 700). Second, Professor Minnich testified that for ID to be considered science, the ground rules of science have to be broadened so that supernatural forces can be considered. (38:97 (Minnich)). Third, Professor Steven William Fuller testified that it is ID’s project to change the ground rules of science to include the supernatural. (Trial Tr. vol. 28, Fuller Test., 20-24, Oct. 24, 2005). Decision, pp.29-30
Moving on, Krauze seems to misunderstand one of the main points that I was trying to make last post:
For TQA, Jones was simply concerned about testability, and supernatural concepts are characterized by a lack of testability.([...] indicates material I've trimmed from the quotes due to length concerns.)I do not think that the supernatural is arbitrarily excluded from science. I believe that supernatural explanations are excluded from science primarily because they are not testable. [...].At this point, however, I sense that TQA is simply substituting his own view of things for that of Judge Jones. Consider the text of the ruling:We find that ID fails on three different levels, any one of which is sufficient to preclude a determination that ID is science. They are: (1) ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; [...]As we will discuss in more detail below, it is additionally important to note that ID has failed to gain acceptance in the scientific community, it has not generated peer-reviewed publications, nor has it been the subject of testing and research.Does anyone reading this come away with the conclusion that the last part of the “additionally important” factiods is really the justification for item number one on Judge Jones’ laundry list of “levels”? Indeed, how can supernaturalness by itself be “sufficient” to rule that intelligent design is unscientific, independent of the criterion that supposedly provides its justification?
When I raised those points about testability and the supernatural, I was not trying to substitute my own reasoning for that of the judge. I was attempting to explain why there is a "centuries-old ground rule" against invoking the supernatural in science. To put it as plainly and simply as possible, nobody has been able to conduct an empirical test for the hypothesis that "God did it," nobody has been able to design an empirical test for the hypothesis that "God did it," and nobody has been able to conceive of an empirical test for the hypothesis that "God did it."
This line of reasoning was available to the judge when he wrote his opinion. Two different experts testified on this during the plaintiff's case. You can find it in Ken Miller's testimony and in Robert Pennock's testimony.
Noting as an "additionally important" fact the lack of positive tests of ID is also relevant. This does not simply restate the untestable nature of supernatural causes; it also provides a strong indication that ID proponents have not been successful in their attempts at overcoming this limitation. To put it another way, in the absence of a method of positively testing for a supernatural cause, there is absolutely no reason whatsoever to reassess the "centuries-old ground rules of science."
In an attempt to move the discussion into more pragmatic grounds, Krauze presents me with a hypothetical:
Let’s say that Dr. Smith has formulated a hypothesis about intelligent design that causes him to form some quite specific expectations, and which he now intends to test. To get his experiment funded, he sends an application to the National Science Foundation (NSF), a federal agency that funds a considerable amount of research. Imagine, then, the reply:
“Your proposal sounds interesting, and we would like to fund your research. However, you cannot make the link to intelligent design explicit when you publish the results. The NSF only supports scientific research, and as a judge in Dover recently found, intelligent design is inherently unscientific.”
I tried to put a little effort into answering this, but, to put it bluntly, I don't find it to be either interesting or realistic. Yes, I think that such a demand from the NSF would be unreasonable, and I think that a scientist in such a situation should strenuously object. I also think that I'll carry an open umbrella with me at all times outdoors if pigs learn how to fly. In both cases, there's something really, really big between the hypothetical that has been posed and current reality.
If you want me to seriously question whether excluding the supernatural is a good ground rule, you are going to need to give me a real reason to reconsider the situation. Come up with a remotely reasonable test, and I'll get interested quick. Until you have that, all of these complaints about how unfair it is to exclude these things are nothing more than sour grapes.
28 December 2005
26 December 2005
More follow-up on naturalism versus supernaturalism
It would appear that I've wound up in an open and vigorous exchange of views with Krauze on the topic of supernaturalism as it relates to Judge Jones' decision on the Intelligent Design issue.
Here's the sequence of posts, if anyone wants to review earlier events:
I started with a post about misrepresentation of the decision by ID proponents.
Krauze pointed out that I had failed to discuss the judge's comments on the supernatural nature of ID.
I attempted to clarify my position on supernaturalism.
Krauze has responded to my response.
The remainder of this post constitutes my response to his response to my response to his response to my initial post. We're a very responsible pair. (Bonus points to anyone outside my immediate family who figures out what movie I'm watching right now.)
Actually, I think these chains of responses can be good, and not just because they let me toss out incredibly weak pop-culture references. For starters, they let you see where the differences of opinion really sit, and where the differences really seem to be more the result of people just talking at cross-purposes to one another. In this case, I think we might be talking past each other more than anything else.
Krauze writes:
Let me see if I can be a bit clearer in response to this than I was last time. I do not think that the supernatural is arbitrarily excluded from science. I believe that supernatural explanations are excluded from science primarily because they are not testable. To the best of our knowledge, based on a long history of scientific investigation, it is quite simply not possible to scientifically test for supernatural causation.
For the moment, I think that the supernatural nature of ID represents perfectly reasonable grounds for ruling it unscientific. It's a fairly quick test to apply, it doesn't seem to yield ambiguous results, and it has very worked well so far. However, things can change, if only in theory. I do not believe that any of the ID proponents will be able to devise a positive test for Intelligent Design. If a positive test is devised, I think that a reasonable argument could be made that ID is no longer a supernatural explanation. But if a positive test is devised for design and if design is still felt by most to be a supernatural explanation, then (and only then) I think it would be reasonable to revisit the question of whether or not supernatural explanations should be excluded from science.
Krauze either misunderstood me the first time, or he thinks that this indicates that I have reservations about the decision:
Here's the sequence of posts, if anyone wants to review earlier events:
I started with a post about misrepresentation of the decision by ID proponents.
Krauze pointed out that I had failed to discuss the judge's comments on the supernatural nature of ID.
I attempted to clarify my position on supernaturalism.
Krauze has responded to my response.
The remainder of this post constitutes my response to his response to my response to his response to my initial post. We're a very responsible pair. (Bonus points to anyone outside my immediate family who figures out what movie I'm watching right now.)
Actually, I think these chains of responses can be good, and not just because they let me toss out incredibly weak pop-culture references. For starters, they let you see where the differences of opinion really sit, and where the differences really seem to be more the result of people just talking at cross-purposes to one another. In this case, I think we might be talking past each other more than anything else.
Krauze writes:
TQA raises an interesting point. You see, the reaction he describes as stubborn and unpragmatic [discarding a specific positively tested ID hypothesis because it is supernaturalistic] is actually the one that Judge Jones’ ruling would have us choose. Remember that any one of the items on Jones’ laundry list was by itself sufficient to declare intelligent design unscientific. So in the hypothetical situation that TQA describes, Judge Jones would still demand that we label intelligent design as an unscientific conjecture, “pragmatic grounds” be damned.
Let me see if I can be a bit clearer in response to this than I was last time. I do not think that the supernatural is arbitrarily excluded from science. I believe that supernatural explanations are excluded from science primarily because they are not testable. To the best of our knowledge, based on a long history of scientific investigation, it is quite simply not possible to scientifically test for supernatural causation.
For the moment, I think that the supernatural nature of ID represents perfectly reasonable grounds for ruling it unscientific. It's a fairly quick test to apply, it doesn't seem to yield ambiguous results, and it has very worked well so far. However, things can change, if only in theory. I do not believe that any of the ID proponents will be able to devise a positive test for Intelligent Design. If a positive test is devised, I think that a reasonable argument could be made that ID is no longer a supernatural explanation. But if a positive test is devised for design and if design is still felt by most to be a supernatural explanation, then (and only then) I think it would be reasonable to revisit the question of whether or not supernatural explanations should be excluded from science.
Krauze either misunderstood me the first time, or he thinks that this indicates that I have reservations about the decision:
What is interesting is that the Dover ruling has been touted as a huge victory for reason and science, and less than a week after, we find TQA - a scientist by his own testimony - having to distance himself from the logic of the court’s findings.I am not in any way distancing myself from the logic in the decision. I merely acknowledge that there is a possibility - a very slim possibility - that at some point in time in the future the ID proponents might be able to come up with a discovery that would invalidate some of the reasoning. Of course, a great deal would have to happen before that point is reached. Not least, the ID folks need to do science.
A follow-up to my Christmas Wish post
I posted a very brief message late Christmas Eve. The message consisted of three words ("Dona nobis pacem"), linked to the Iraq casualties page. There are only two responses to this message on the blog, both from my brothers. Off the blog, I have received a few more responses sent via email. These were much less pleasant.
That one post was apparently enough to brand me a "trator" in the eyes of some. Suggesting that there is a real reason to wish for peace makes me a coward, willing to "sell out our brave troops to score a petty little political point." Wow. I had no idea that hoping that people stop dying is an act of such cowardice.
I suppose I'd better apologize to my wife, my brother Ben, my brother-in-law Ricky, every household in my neighborhood, and countless other people I know for "selling out." Guys, I'm real sorry that I dared to publicly wish that you won't need to put your lives on the line in a combat zone during the new year.
People who think that wishing for peace sells out the troops are probably the single greatest argument I can think of in favor of restoring the draft, because those people are almost definitely the ones who don't know anyone in the service.
I'm sure that they haven't had to deal with the knowledge that someone in a loved one's unit has died, and notifications will be taking place shortly. I'm sure that they haven't had to remember that on a day like that you make sure to phone your next door neighbor before going over, just to make sure that they aren't startled by your knock. (The casualty notifications come as a knock without prior warning.) I'm sure that they haven't felt the blessed mixture of relief and guilt when their prayers that it was someone else's loved one are answered.
Wishing for peace is not a sign of fear or weakness. Wishing for peace is simply a symptom of humanity.
That one post was apparently enough to brand me a "trator" in the eyes of some. Suggesting that there is a real reason to wish for peace makes me a coward, willing to "sell out our brave troops to score a petty little political point." Wow. I had no idea that hoping that people stop dying is an act of such cowardice.
I suppose I'd better apologize to my wife, my brother Ben, my brother-in-law Ricky, every household in my neighborhood, and countless other people I know for "selling out." Guys, I'm real sorry that I dared to publicly wish that you won't need to put your lives on the line in a combat zone during the new year.
People who think that wishing for peace sells out the troops are probably the single greatest argument I can think of in favor of restoring the draft, because those people are almost definitely the ones who don't know anyone in the service.
I'm sure that they haven't had to deal with the knowledge that someone in a loved one's unit has died, and notifications will be taking place shortly. I'm sure that they haven't had to remember that on a day like that you make sure to phone your next door neighbor before going over, just to make sure that they aren't startled by your knock. (The casualty notifications come as a knock without prior warning.) I'm sure that they haven't felt the blessed mixture of relief and guilt when their prayers that it was someone else's loved one are answered.
Wishing for peace is not a sign of fear or weakness. Wishing for peace is simply a symptom of humanity.
24 December 2005
A quick Christmas Thought.
Looking over things that I am wrapping today and will be helping with tomorrow, I've reached the conclusion that the six most obscene words in the English language are, "some assembly required, batteries not included."
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